What Makes a Good (Computed) Energy Profile?

2020 ◽  
pp. 1-38
Author(s):  
Odile Eisenstein ◽  
Gregori Ujaque ◽  
Agustí Lledós
Keyword(s):  
Energy Profile

Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

2019 ◽  
Author(s):  
Bella Grigorenko ◽  
Igor Polyakov ◽  
Alexander Nemukhin
Keyword(s):  
Adenylyl Cyclase ◽  
Bond Cleavage ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Md Simulations ◽  
Coordination Shell ◽  
Energy Profile ◽  
One Step ◽  
Type V

<p>We report a mechanism of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) conversion by the mammalian type V adenylyl cyclase revealed in molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations. We characterize a set of computationally derived enzyme-substrate (ES) structures showing an important role of coordination shells of magnesium ions in the solvent accessible active site. Several stable six-fold coordination shells of Mg<sub>A</sub><sup>2+ </sup>are observed in MD simulations of ES complexes. In the lowest energy ES conformation, the coordination shell of Mg<sub>A</sub><sup>2+ </sup>does not include the O<sub>δ1</sub> atom of the conserved Asp440 residue. Starting from this conformation, a one-step reaction mechanism is characterized which includes proton transfer from the ribose O<sup>3'</sup>H<sup>3' </sup>group in ATP to Asp440 via a shuttling water molecule and P<sup>A</sup>-O<sup>3A</sup> bond cleavage and O<sup>3'</sup>-P<sup>A</sup> bond formation. The energy profile of this route is consistent with the observed reaction kinetics. In a higher energy ES conformation, Mg<sub>A</sub><sup>2+</sup> is bound to the O<sub>δ1</sub>(Asp440) atom as suggested in the relevant crystal structure of the protein with a substrate analog. The computed energy profile initiated by this ES is characterized by higher energy expenses to complete the reaction. Consistently with experimental data, we show that the Asp440Ala mutant of the enzyme should exhibit a reduced but retained activity. All considered reaction pathways include proton wires from the O<sup>3'</sup>H<sup>3' </sup>group via shuttling water molecules. </p>

Survey for Transition of Normal Reaction

2018 ◽  
Vol 5 (3) ◽  
Author(s):  
Hassan Akbari Rahimi
Keyword(s):  
Transition State ◽  
Reactive Intermediates ◽  
The State ◽  
Energy Profile ◽  
Normal Reaction ◽  
Unstable Molecules ◽  
The Difference ◽  
Bond Vibration ◽  
Unstable Molecule ◽  
Profile Diagram

Transition of reaction is a short-lived unstable molecule in a reaction which is formed in between the reaction when reactants change into products. Whereas, transition state is just the state before formation of new molecule (involves breaking of bonds of reactants and formation of new ones) Transition of reaction differs from a transition state in that the intermediate has a discrete lifetime (be it a few nanoseconds or many days), whereas a transition state lasts for just one bond vibration cycle. Intermediates may be unstable molecules (in which case they are called reactive intermediates) or highly stable molecules. The difference between them can be better described through the energy profile diagram.

Energy Profile Summary for North River WWTP Cogeneration Upgrades

2015 ◽  
Vol 2015 (2) ◽  
pp. 1-28
Author(s):  
Tia Trate ◽  
Stephen Tarallo ◽  
Anthony Fiore ◽  
James Lauria
Keyword(s):  
Energy Profile

Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

2021 ◽  
Author(s):  
Norifumi Yamamoto
Keyword(s):  
Free Energy ◽  
Profile Analysis ◽  
Energy Profile ◽  
Contributing Factors ◽  
Free Energy Profile ◽  
Aggregation Induced Emission ◽  
Energy Profiles ◽  
Free Energy Profiles

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

Primary and Secondary Isotope Effects in the Photooxidation of 2,5-Dimethyl-2,4-hexadiene. Elucidation of the Reaction Energy Profile

1998 ◽  
Vol 63 (18) ◽  
pp. 6390-6393 ◽  
Author(s):  
Georgios Vassilikogiannakis ◽  
Manolis Stratakis ◽  
Michael Orfanopoulos
Keyword(s):  
Isotope Effects ◽  
Energy Profile ◽  
Reaction Energy

scholarly journals Nonequilibrium study of the intrinsic free-energy profile across a liquid-vapour interface

2016 ◽  
Vol 144 (4) ◽  
pp. 044703 ◽  
Author(s):  
Carlos Braga ◽  
Jordan Muscatello ◽  
Gabriel Lau ◽  
Erich A. Müller ◽  
George Jackson
Keyword(s):  
Free Energy ◽  
Energy Profile ◽  
Free Energy Profile
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